Egypt's upcoming military deployment to Somalia will worsen tensions with Ethiopia, whose own frictions with Mogadishu raise the risk of clashes between Egyptian and Ethiopian forces in Somalia, leading to security vacuums that insurgents will likely exploit. On Oct. 10, Somalia, Egypt and Eritrea signed a deal to enhance their security cooperation. This was the latest sign of both Egypt's growing ties with Somalia and frictions with Ethiopia, following the August announcement that Egypt would contribute approximately 5,000 troops to the new African Union Support and Stabilization Mission in Somalia (AUSSOM), set to begin on Jan. 1. This mission, with at least 10,000 personnel, will replace the African Union Transition Mission in Somalia (ATMIS), and will primarily focus on counterterrorism operations against the al Qaeda-affiliated group al Shabaab. This development came amid a growing diplomatic dispute between Ethiopia and Somalia, sparked by Ethiopia's controversial decision in January to sign a deal with Somaliland, a breakaway region of Somalia, to grant Ethiopia access to the Red Sea port of Berbera for both commercial and military purposes. In response to the situation, Somalia, citing a breach of its sovereignty, threatened to expel 8,000 to 10,000 Ethiopian troops stationed primarily in Somalia's Jubaland and South West states, who have been crucial in countering al Shabaab, if Ethiopia did not scrap its agreement with Somaliland. These troops have so far not been expelled, but Mogadishu has set a deadline for the end of the year.

• In addition to contributing trips to AUSSOM, reports indicate that Egypt is also considering deploying more troops to Somalia on a bilateral level. 
• ATMIS, which had 17,500 troops deployed in Somalia as of September 2024, is leaving the country to transition security responsibilities to the Somali National Army as part of a strategic plan to build local military capacity. However, Somali forces are still far from being capable of handling al Shabaab on their own, which is why AUSSOM is set to replace ATMIS in 2025.

These developments, amid broader tensions between Egypt and Ethiopia over the Nile River and Somalia's internal governance fissures and ongoing insurgencies, could worsen regional security as the impending expulsion of Ethiopian troops diminishes efforts against al Shabaab and Islamic State Somalia Province (ISSP). Egypt's pledged troop deployment to Somalia, ​​along with the Oct. 10 agreement between Somalia, Eritrea and Egypt to enhance security cooperation amid tensions with Ethiopia, are not just related to the Ethiopia-Somaliland port deal but also Egypt's concerns over the filling of Ethiopia's Grand Ethiopian Renaissance Dam (GERD) on the Nile River, with negotiations on the issue having stalled. Ethiopia views the dam as essential for generating electricity and boosting its economy, though Egypt fears it will reduce the river's flow and threaten its water security, given that Egypt relies on the Nile for over 90% of its freshwater. Somalia's burgeoning security cooperation with Egypt also comes at a time when Mogadishu is facing governance challenges with its federal states, mainly Jubaland and South West, as well as the semi-autonomous regions of Puntland and Somaliland, the latter having declared independence. The leaders in Jubaland and South West have expressed concerns over the federal government's threat to expel Ethiopian troops, who they argue are essential for countering al Shabaab in their states. Since AUSSOM is designed to deploy fewer troops than ATMIS, new troops unfamiliar with the Somali threat environment will need time to adjust and will likely face at least initial challenges in combating al Shabaab as they struggle to replace the knowledge and experience of Ethiopian forces, who have been in Somalia for years. Meanwhile, Puntland is grappling with its own internal security challenges, particularly with the rise of ISSP, which has gained a foothold in Putland's Bari region. The strained relationship between Puntland and the Somali federal government, driven by disputes over resource sharing and March constitutional changes, has further complicated intelligence coordination and counterterrorism efforts to tackle the Islamic State affiliate.

• In March 2024, Somalia's federal parliament approved amendments enhancing presidential authority and introducing direct universal suffrage. This prompted Puntland to withdraw its recognition of the federal government, citing a lack of consultation, which has since increased tensions between the semi-autonomous region and Mogadishu. 
• Regional leaders in Somalia's Jubaland and South West states have also criticized the constitutional changes, echoing Puntland's concerns by arguing the amendments were made without adequate consultation and infringed upon their states' autonomy.

Tensions between Mogadishu and Somali states over power-sharing and governance will likely worsen, with Egypt's military support to the federal government risking further instability by deepening local grievances and weakening regional cooperation. Ongoing disputes over power-sharing, resource distribution and governance between the Somali federal government and its member states are set to escalate, as the former's efforts to enhance control run up against the latter's push for greater autonomy and local governance, deepening distrust between them. Though individual states cannot officially dictate whether Ethiopian troops leave, the federal government may struggle to assert its authority over the states, particularly in South West and Jubaland, where local administrations will likely continue pursuing independent agendas that conflict with federal policies, such as the maintenance of Ethiopian troops in their territories. Furthermore, Somalia's burgeoning relationship with Egypt could further complicate these dynamics, as any military assistance and personnel that Cairo provides to Mogadishu may be perceived as an attempt to bolster federal authority at the expense of Somali member states' autonomy, especially amid the looming departure of Ethiopian troops against their will. Local leaders in South West and Jubbaland, in particular, may see federal support from Egypt as encroachment on their own power, exacerbating their existing grievances and mistrust, while undermining cooperative governance efforts. Additionally, Putland's ongoing disputes with the Somali federal government could undermine efforts to counter ISSP activity in the region by hindering intelligence sharing and coordination. This could enable the jihadist group to expand its presence in Putland, including by recruiting more foreign fighters, some of whom could potentially return to their home countries, such as Ethiopia, to launch attacks. 

• During an interview with Voice of America published on Oct. 2, the U.S. Commander of AFRICOM claimed that ISSP has doubled in size over the past year. Other reports suggest that ISSP has approximately 500 members, half of whom are foreign nationals primarily based in the Cal-Miskaat Mountains of Puntland's Bari region. Many of these foreign fighters hail from East Africa, particularly Ethiopia, Kenya and Tanzania, though a few also come from Arab countries like Yemen.

The formalization of the port deal between Somaliland and Ethiopia would escalate tensions and raise the risk of Ethiopian troops clashing with Somali forces and, in a more escalatory scenario, Egyptian soldiers, potentially leading to a proxy war in which Somalia supports Ethiopian rebels. Should Somaliland and Ethiopia formalize the port deal, the diplomatic dispute between Ethiopia and Somalia would significantly increase. This would raise the risk of physical confrontations characterized by skirmishes between Somali federal forces and Ethiopian troops in Somalia, as the former attempts to push the latter out of Jubaland and South West. If this situation intensifies and skirmishes become frequent, Ethiopia may conduct incursions into Somalia, which, if they occur after Egypt has deployed troops to Somalia, could lead to clashes between Egyptian and Ethiopian forces under the pretext of Egypt protecting Somalia's sovereignty. Moreover, such an escalation would increase the likelihood of a proxy war in Ethiopia — especially if the Ethiopian federal government's 2018 peace deal with the Ogaden National Liberation Front (ONLF), which aims for autonomy in Ethiopia's Somali region, were to collapse and enable ONLF to act as a proxy for Somalia, thereby intensifying the conflict in Ethiopia. While this agreement is unlikely to collapse in the near term, tensions between the ONLF and the Ethiopian government in Addis Ababa could resurface due to unresolved grievances over autonomy and resource allocation, potentially leading the ONLF to re-emerge as a militant force. Furthermore, if the ONLF were to receive support from Somalia, this could create a direct link between the two conflicts (namely, that between Ethiopia and Somalia over the port deal, and that between Ethiopia and Egypt over the Nile River), prompting the Ethiopian federal government to view the ONLF's actions not merely as a local issue but as a broader threat tied to Somali interests. Under this perception, Ethiopia might use increased military force against the ONLF, which would only escalate violence and instability. Additionally, in September, Somalia's foreign affairs minister expressed that the Somali government may support Ethiopian rebels if Ethiopia refuses to scrap its port deal with Somaliland. This raises the possibility of Somalia backing the various groups in Ethiopia seeking autonomy in their respective regions, including Amhara, Fano and Oromo militants, all of whom oppose the Ethiopian federal government. Somali support in the form of weapons or funding could enhance these groups' capabilities to launch more large-scale attacks, increase clashes with Ethiopian federal forces and escalate kidnappings, thereby destabilizing Ethiopia's Amhara and Oromia regions.

• The 2018 peace deal between the Ethiopian federal government and the ONLF marked the official end of a decades-long insurgency in Ethiopia's Somali region. The ONLF agreed to lay down arms and engage in peaceful political processes. However, unresolved grievances over autonomy and resource allocation, combined with potential external support for the ONLF and a heavy-handed response from the Ethiopian government, could jeopardize the agreement and lead to a resurgence of conflict.
• Should Somalia decide to back Ethiopian rebels or the ONLF, it is unlikely to be the sole provider of support, as weapons are cheap and readily available on the black market, and the Somali diaspora could also raise funds for the ONLF or other rebels.
• A proxy war in Ethiopia involving the ONLF would also risk escalating ethnic tensions in Somalia, leading to increased radicalization and possible clan violence. 

If Ethiopia fails to withdraw its troops from Somalia, clashes with Somali federal forces or, in a more escalatory scenario, with Egyptian forces are likely, creating a security vacuum that al Shabaab will likely exploit to launch further attacks in Somalia and neighboring countries. If Egyptian and Ethiopian troops were to clash in Somalia's Jubaland and South West states, al Shabaab would likely seize the opportunity to add to the chaos by launching large-scale attacks in Somalia, targeting regions along the border with neighboring Kenya and even Ethiopia, while reclaiming some territories previously held by Somali federal forces in the south. The presence of AUSSOM forces would help mitigate the security vacuum to some extent, though efforts would likely focus on protecting the capital, Mogadishu, and maintaining control over key areas under the federal government's jurisdiction — thereby leaving wide swathes of Somalia exposed to al Shabaab attacks and territorial seizures.